[SOLVED] How to enable Clean URLs ?

On CentOs 6.3 where not using .htaccess and using instead mysubname.conf in /etc/httpd/conf.d included in httpd.conf

On login the url directs to /?=admin/config/search/clean-urls and test fails but if change directory in url bar to
/admin/config/search/clean-urls the checkbox appears but when checked it doesn't save checked.

Below is the mysubname.conf which is basically everything in the .htaccess file plus virtualhost directory.

#
# Apache/PHP/Drupal settings:
#

# Protect files and directories from prying eyes.
<FilesMatch "\.(engine|inc|info|install|make|module|profile|test|po|sh|.*sql|theme|tpl(\.php)?|xtmpl)$|^(\..*|Entries.*|Repository|Root|Tag|Template)$">
  Order allow,deny
</FilesMatch>

# Don't show directory listings for URLs which map to a directory.
Options -Indexes

# Follow symbolic links in this directory.
Options +FollowSymLinks

# Make Drupal handle any 404 errors.
ErrorDocument 404 /index.php

# Set the default handler.
DirectoryIndex index.php index.html index.htm

# Override PHP settings that cannot be changed at runtime. See
# sites/default/default.settings.php and drupal_environment_initialize() in
# includes/bootstrap.inc for settings that can be changed at runtime.

# PHP 5, Apache 1 and 2.
<IfModule mod_php5.c>
  php_flag magic_quotes_gpc                 off
  php_flag magic_quotes_sybase              off
  php_flag register_globals                 off
  php_flag session.auto_start               off
  php_value mbstring.http_input             pass
  php_value mbstring.http_output            pass
  php_flag mbstring.encoding_translation    off
</IfModule>

# Requires mod_expires to be enabled.
<IfModule mod_expires.c>
  # Enable expirations.
  ExpiresActive On

  # Cache all files for 2 weeks after access (A).
  ExpiresDefault A1209600

  <FilesMatch \.php$>
    # Do not allow PHP scripts to be cached unless they explicitly send cache
    # headers themselves. Otherwise all scripts would have to overwrite the
    # headers set by mod_expires if they want another caching behavior. This may
    # fail if an error occurs early in the bootstrap process, and it may cause
    # problems if a non-Drupal PHP file is installed in a subdirectory.
    ExpiresActive Off
  </FilesMatch>
</IfModule>

# Various rewrite rules.
<IfModule mod_rewrite.c>
  RewriteEngine on

  
  RewriteRule "(^|/)\." - [F]

 
  # Pass all requests not referring directly to files in the filesystem to
  # index.php. Clean URLs are handled in drupal_environment_initialize().

<Directory /var/www/html/mysubname.site.net>
RewriteEngine on
RewriteBase /mysubname
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} ^/mysubname/(.*)$
RewriteRule ^(.*)$ /mysubname/index.php?q=$1 [L,QSA]

RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteCond %{REQUEST_URI} !=/favicon.ico
  RewriteRule ^index.php [L]

</Directory>

  # Rules to correctly serve gzip compressed CSS and JS files.
  # Requires both mod_rewrite and mod_headers to be enabled.
  <IfModule mod_headers.c>
    # Serve gzip compressed CSS files if they exist and the client accepts gzip.
    RewriteCond %{HTTP:Accept-encoding} gzip
    RewriteCond %{REQUEST_FILENAME}\.gz -s
    RewriteRule ^(.*)\.css $1\.css\.gz [QSA]

    # Serve gzip compressed JS files if they exist and the client accepts gzip.
    RewriteCond %{HTTP:Accept-encoding} gzip
    RewriteCond %{REQUEST_FILENAME}\.gz -s
    RewriteRule ^(.*)\.js $1\.js\.gz [QSA]

    # Serve correct content types, and prevent mod_deflate double gzip.
    RewriteRule \.css\.gz$ - [T=text/css,E=no-gzip:1]
    RewriteRule \.js\.gz$ - [T=text/javascript,E=no-gzip:1]
#my rules
NameVirtualHost *:80

<VirtualHost *:80>
ServerName site.net
ServerAlias www.site.net
ServerAdmin admin@site.net
DocumentRoot "/var/www/html"
<Directory /var/www/html/www.site.net/>
AllowOverride All
Allow from all
</Directory>
</VirtualHost>

<VirtualHost *:80>
ServerName mysubname.site.net
ServerAlias www.mysubname.site.net
ServerAdmin admin@mysubname.site.net
VirtualDocumentRoot "/var/www/html/mysubname"
</VirtualHost>

ServerName localhost

<Directory /var/www/html/mysubname>
  AllowOverride All
RewriteBase /mysubname
</Directory>


    <FilesMatch "(\.js\.gz|\.css\.gz)$">
      # Serve correct encoding type.
      Header set Content-Encoding gzip
      # Force proxies to cache gzipped & non-gzipped css/js files separately.
      Header append Vary Accept-Encoding
    </FilesMatch>
  </IfModule>
</IfModule>

@roblog that code didn't work for me.